Lab 5 Extra: Interactive Graphs and Animations from the COVID-19 reporting data

More information related to this lab can be found here.

Challenge Exercises

Students in the 697 class need to complete the following challenges.

Challenge Exercise 1

Print a graph to a png file using 3*ppi for the height and width and display the png file in the report using the above R Markdown format.

library(tidyverse)

time_series_confirmed <- read_csv(url("https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_global.csv")) %>%
  rename(Province_State = "Province/State", Country_Region = "Country/Region") %>%
  mutate(report_type = "confirmed_cases") %>%
  select(report_type, everything())

head(time_series_confirmed)

library(tidyverse)

time_series_deaths <- read_csv(url("https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_deaths_global.csv")) %>%
  rename(Province_State = "Province/State", Country_Region = "Country/Region") %>%
  mutate(report_type = "confirmed_deaths") %>%
  select(report_type, everything())

head(time_series_deaths)

library(tidyverse)

time_series_joined <- bind_rows(time_series_confirmed, time_series_deaths) %>%
  gather(key="date", value="count", 6:length(.)) %>%
  mutate(date=lubridate::mdy(date)) %>%
  spread(key="report_type", value="count") %>%
  mutate(confirmed_cases=replace_na(confirmed_cases, 0),
         confirmed_deaths=replace_na(confirmed_deaths, 0))

head(time_series_joined)
tail(time_series_joined)

library(tidyverse)

time_series_sum <- time_series_joined %>%
  group_by(date) %>%
  summarize(cases = sum(confirmed_cases),
            deaths = sum(confirmed_deaths)) %>%
  mutate(deaths_cases = deaths/cases)

head(time_series_sum)

library(tidyverse)

time_series_sum <- time_series_joined %>%
  filter(Country_Region=="US") %>%                      #| Filter only US Data
  group_by(date) %>%
  summarize(cases = sum(confirmed_cases),
            deaths = sum(confirmed_deaths)) %>%
  mutate(deaths_cases = deaths/cases)

ppi=300

library(ggplot2)

p1 <- ggplot(time_series_sum, aes(x=date, y=deaths_cases)) +
  geom_line() +
  labs(x="", y="Deaths/Cases", title="Fatality Rate in the U.S.") +
  theme_linedraw() +
  theme(plot.title=element_text(face="bold", hjust=0.5),
        panel.grid.major=element_blank(),
        panel.grid.minor=element_blank())

png("/Users/greg/Box/courses/umass/fall-2020/evolutionary-genomics-and-bioinformatics/evo-geno-course/images/fatality-rate-in-the-usa-plot.png", 
    width=3*ppi, height=3*ppi, res=ppi)

p1

dev.off()

Challenge Exercise 2

Turn one of the exercises from Lab 5 into an interactive graph with plotyly.

library(ggplot2)
library(plotly)

p1 <- ggplot(time_series_sum, aes(x=date, y=deaths_cases)) +
  geom_line() +
  labs(x="", y="Deaths/Cases", title="Fatality Rate in the U.S.") +
  theme_linedraw() +
  theme(plot.title=element_text(face="bold", hjust=0.5),
        panel.grid.major=element_blank(),
        panel.grid.minor=element_blank())

ggplotly(p1)

Challenge Exercise 3

Create an animated graph of your choosing using the time series data to display an aspect (e.g. states or countries) of the data that is important to you.

library(tidyverse)

time_series_confirmed <- read_csv(url("https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_US.csv")) %>%
  select(7:length(.)) %>%
  gather(key="date", value="cases", 6:length(.)) %>%
  mutate(date = lubridate::mdy(date)) %>%
  group_by(date, Province_State) %>%
  summarize(total_cases = sum(cases)) %>%
  filter(Province_State %in% c("Pennsylvania", "Washington", "Massachusetts"))

head(time_series_confirmed)

library(ggplot2)
library(gganimate)
library(transformr)
library(gifski)

p1 <- ggplot(time_series_confirmed, aes(x=date, y=total_cases)) +
  labs(x="", y="confirmed cases", title="COVID-19 Cases by State") +
  geom_line(aes(color=Province_State)) +
  theme_linedraw() +
  theme(plot.title=element_text(face="bold", hjust=0.5),
        panel.grid.major=element_blank(),
        panel.grid.minor=element_blank(),
        legend.position="bottom",
        legend.title=element_blank()) +
  transition_reveal(date)

animate(p1, renderer = gifski_renderer(), end_pause = 15)